RetrogeneDB ID: retro_cjac_550

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:76075135..76075438(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022849
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ENY2
• Ensembl ID: ENSCJAG00000006389
• Aliases: None
• Description: enhancer of yellow 2 homolog (Drosophila) [Source:HGNC Symbol;Acc:24449]

Sequence

>retro_cjac_550
ATGGTGGTTAGCAAAATGAACAAAGATGCGCAGATGAGAGCAGCGATTAACCAAAAGTTGATGGAAACTGGAGAAAGAGA
ACGTCTCAGAGAGTTGCTGAGAGCTAAATTAATTGAATGTGGCTGGAAGGATCAGCTGAAGGCACACTGTAAAGAGATAA
TTAAAGAAAAAGGACTAGAACACGTTACTGTTGGTGACTTGGTGGCTGAAATCACTCCAAAAGGCAGAGCCCTGGTACCT
GACAGTGTAAAGAAGGAGCTCCTACAAAGAATAAGAACATTCCTTGCTCAGCATGCCAGCCTT

Alignment

ORF - retro_cjac_550 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVVSKMNKDAQMRAAINQKLIETGERERLKELLRAKLIECGWKDQLKAHCKEVIKEKGLEHVTVDDLVAE
          MVVSKMNKDAQMRAAINQKL.ETGERERL.ELLRAKLIECGWKDQLKAHCKE.IKEKGLEHVTV.DLVAE
Retrocopy MVVSKMNKDAQMRAAINQKLMETGERERLRELLRAKLIECGWKDQLKAHCKEIIKEKGLEHVTVGDLVAE

Parental  ITPKGRALVPDSVKKELLQRIRTFLAQHASL
          ITPKGRALVPDSVKKELLQRIRTFLAQHASL
Retrocopy ITPKGRALVPDSVKKELLQRIRTFLAQHASL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.53 RPM	6.99 RPM
SRP051959_heart	0.21 RPM	8.21 RPM
SRP051959_kidney	0.13 RPM	15.49 RPM
SRP051959_liver	0.19 RPM	15.68 RPM
SRP051959_lung	0.34 RPM	7.34 RPM
SRP051959_lymph_node	0.43 RPM	6.21 RPM
SRP051959_skeletal_muscle	0.22 RPM	9.19 RPM
SRP051959_spleen	0.34 RPM	9.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_550 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_550 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003039	1 retrocopy	retro_acar_1,
Callithrix jacchus	ENSCJAG00000006389	4 retrocopies	retro_cjac_1206, retro_cjac_1355, retro_cjac_1436, retro_cjac_550 ,
Cavia porcellus	ENSCPOG00000010988	1 retrocopy	retro_cpor_927,
Dasypus novemcinctus	ENSDNOG00000007377	1 retrocopy	retro_dnov_25,
Echinops telfairi	ENSETEG00000010882	2 retrocopies	retro_etel_1826, retro_etel_450,
Microcebus murinus	ENSMICG00000012948	3 retrocopies	retro_mmur_1041, retro_mmur_773, retro_mmur_793,
Myotis lucifugus	ENSMLUG00000027585	1 retrocopy	retro_mluc_357,
Macaca mulatta	ENSMMUG00000006104	2 retrocopies	retro_mmul_1094, retro_mmul_1490,
Pongo abelii	ENSPPYG00000025888	1 retrocopy	retro_pabe_750,
Sarcophilus harrisii	ENSSHAG00000001787	4 retrocopies	retro_shar_454, retro_shar_675, retro_shar_815, retro_shar_816,
Tupaia belangeri	ENSTBEG00000000273	4 retrocopies	retro_tbel_2257, retro_tbel_324, retro_tbel_4307, retro_tbel_823,
Tursiops truncatus	ENSTTRG00000001742	3 retrocopies	retro_ttru_46, retro_ttru_845, retro_ttru_997,